Positions

Staff Member

2010 - present

Carnegie Institution, Dept. of Embryology

Adjunct Assistant Professor

2010 - present

Johns Hopkins University, Dept. of Biology

Adjunct Assistant Professor

2010 - present

Johns Hopkins Medical Institute, Dept. of Molecular Biology and Genetics
Education

University of California—San Francisco

Postdoctoral fellow

Harvard University

Ph.D., Biology, 2006

Thesis: Bistability and positive feedback in genetic networks

Massachusetts Institute of Technology

S.B., Biology, 2000

S.B., Mathematics, 2000

Research Experience

University of California—San Francisco

2006 - 2010

Postdoctoral Fellow, Dept. of Cellular and Molecular Pharmacology
Advisor: Jonathan Weissman

Harvard University

2000 - 2006

Graduate student researcher, Dept. of Molecular and Cellular and Biology
Advisor: Andrew Murray

Massachusetts Institute of Technology

1997 - 2000

Undergraduate student researcher, Laboratory for Computer Science
Advisor: Bonnie Berger
Undergraduate student researcher, Department of Biology
Advisor: Leonard Guarente
Fellowships and Honors
Searle Scholar (2011 - 2014)
NIH NRSA postdoctoral fellowship (April 2007 - Sept 2009; F32GM080853)
Howard Hughes Medical Institute predoctoral fellowship (Sept 2000 - Aug 2006)
NSF graduate research fellowship (declined)
Phi Beta Kappa, MIT (2000)
Nakatsu F, Baskin JM, Chung J, Tanner LB, Shui G, Lee SY, Pirruccello M, Hao M, Ingolia NT, Wenk MR, De Camilli P. PtdIns4P synthesis at the plasma membrane and its impact on PtdIns(4,5)P2 dynamics to control plasma membrane identity. J Cell Biol 199: 1003 (2012).
Stern-Ginossar N, Weisburd B, Michalski A, Le VT, Hein MY, Huang SX, Ma M, Shen B, Qian SB, Hengel H, Mann M, Ingolia NT, Weissman JS. Decoding human cytomegalovirus. Science 338: 1088 (2012).
Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nature Protocols 7: 1534 (2012).
Michel AM, Roy Choudhury K, Firth AE, Ingolia NT, Atkins JF, Baranov PV. Observation of dually decoded regions of the human genome using ribosome profiling data. Genome Res, published online 16 May 2012.
Hsieh AC, Liu Y, Edlind MP, Ingolia NT, Janes MR, Sher A, Shi EY, Stumpf CR, Christensen C, Bonham MJ, Wang S, Ren P, Martin M, Jessen K, Feldman ME, Weissman JS, Shokat KM, Rommel C, Ruggero D. The translational landscape of mTOR signalling steers cancer initiation and metastasis. Nature 485: 55 (2012).
Brar GA, Yassour M, Friedman N, Regev A, Ingolia NT, Weissman JS. High-Resolution View of the Yeast Meiotic Program Revealed by Ribosome Profiling. Science 335: 552 (2012).
Ingolia NT, Lareau LF, Weissman JS. Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes. Cell 147: 789 (2011).
Gracheva EO, Cordero-Morales JF, Gonzalez-Carcacia JA, Ingolia NT, Manno C, Aranguren CI, Weissman JS, Julius D. Ganglion-specific splicing of TRPV1 underlies infrared sensation in vampire bats. Nature 476: 88 (2011).
Takacs JE, Neary TB, Ingolia NT, Saini AK, Martin-Marcos P, Pelletier J, Hinnebusch AG, Lorsch JR. Identification of compounds that decrease the fidelity of start codon recognition by the eukaryotic translational machinery. RNA 17: 439 (2011).
Guo H, Ingolia NT, Weissman JS, Bartel DP. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466: 835 (2010).
Gracheva EO*, Ingolia NT*, Kelly YM, Cordero-Morales JF, Hollopeter G, Chesler AT, Sánchez EE, Perez JC, Weissman JS, Julius D. Molecular basis of infrared detection by snakes. Nature 464: 1006 (2010).
Bassik MC, Lebbink RJ, Churchman LS, Ingolia NT, Patena W, LeProust EM, Schuldiner M, Weissman JS, McManus MT. Rapid creation and quantitative monitoring of high coverage shRNA libraries. Nature Methods: 6: 443 (2009).
Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324: 218 (2009).
Ingolia NT, Murray AW. Positive-feedback loops as a flexible biological module. Curr Biol. 17: 668 (2007).
Ingolia NT. Topology and robustness in the Drosophila segment polarity network. PLoS Biol. 2: e123 (2004).
* denotes equal contribution
† denotes corresponding or co-corresponding authorship
Reviews
Ingolia NT. Many Paths to the Same End: Histone Transcripts Recruit Canonical Initiation Factors through Unconventional Interactions. Mol Cell 41: 133 (2011).
Fordyce P, Ingolia N. Integrating systems biology data to yield functional genomics insights. Genome Biology 12: 302 (2011).
Ingolia NT. Genome-wide translational profiling by ribosome footprinting. Methods Enzymol 470: 119 (2010).
Ingolia NT, Weissman JS. Systems biology: Reverse engineering the cell. Nature 454: 1059 (2008).
Ingolia NT, Murray AW. The ups and downs of modeling the cell cycle. Curr Biol. 14: R771 (2004).
Ingolia NT, Murray AW. Signal transduction. History matters. Science 297: 948 (2002).
Talks
"Genome-wide Profiling of Translation Initiation and Protein Synthesis." RNA Biology Annual Symposium, The Ohio State University, Columbus, OH. May 2013 (accepted).
"Genome-wide Profiling of Translation Initiation and Protein Synthesis." Department of Biology, Columbia University, New York, NY. February 2013 (accepted).
"Genome-wide Profiling of Translation Initiation and Protein Synthesis." Joint Seminar Series, Thomas Jefferson University, Philadelphia, PA. December 2012.
"Genome-wide Profiling of Translation Initiation and Protein Synthesis." Current Biology Seminar, Fred Hutchinson Cancer Research Center, Seattle, WA. November 2012.
"Genome-wide Profiling of Translation Initiation and Protein Synthesis." Seattle BioMed, Seattle, WA. November 2012.
"Genome-wide Profiling of Translation Initiation and Protein Synthesis." Biochemistry and Biophysics Center, NHLBI, National Institutes of Health, Bethesda, MD. October 2012.
"Genome-wide Profiling of Translation Initiation and Protein Synthesis." Department of Biology, Wesleyan University, Wesleyan, CT. September 2012.
"Genome-wide Profiling of Translation Initiation and Protein Synthesis." Meeting on RNA Sciences in Cell and Developmental Biology, RIKEN Center for Developmental Biology, Kobe, Japan. June 2012.
"Genome-wide Profiling of Translation Initiation and Protein Synthesis." Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD. April 2012.
"Genome-wide Profiling of Translation Initiation and Protein Synthesis." Department of Cell Biology, Johns Hopkins Medical Institute, Baltimore, MD. March 2012.
"Genome-wide Profiling of Translation Initiation and Protein Synthesis." Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH. March 2012.
"Genome-wide Profiling of Translation Initiation and Protein Synthesis." Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY. February 2011.
"Genome-wide Profiling of Translation Initiation and Protein Synthesis." Department of Genetics, North Carolina State University, Raleigh, NC. October 2011.
"Genome-wide Profiling of Translation Initiation and Protein Synthesis." International Institute of Molecular and Cell Biology, Warsaw, Poland. September 2011.
"Genome-wide Profiling of Translation Initiation and Protein Synthesis." Bioinformatics Seminar Series, University of Iowa, Iowa City, IA. April 2011.
"Genome-wide Profiling of Translation Initiation and Protein Synthesis." CSH Asia Conference on High Throughput Biology, Suzhou, China. April 2011.
"Genome-wide Profiling of Translation Initiation and Protein Synthesis." NICHD, National Institutes of Health, Bethesda, MD. April 2011.
"Genome-wide Profiling of Translation Initiation and Protein Synthesis." Computational Biology and Genomics seminar, University of Maryland, College Park, MD. December 2010.
"Genome-Wide Translational Profiling by Ribosome Footprinting." Annual Meeting of the Oligonucleotide Theraputics Society, Dana Point, CA. October 2010.
"Genome-Wide Profiling of Translation Initiation and Elongation." Frontiers in Quantitative Biology, Stanford University School of Medicine, Palo Alto, CA. September 2010.
"Genome-Wide Translational Profiling by Ribosome Footprinting." Department of Human Genetics seminar, University of Utah, Salt Lake City, UT. May 2010.
"Genome-wide analysis of in vivo translation with single-nucleotide resolution." Lorne Genome, Lorne, Australia. February 2010.
"Genome-wide translational profiling of the eIF2α-mediated stress response with single-nucleotide precision." ASCB Annual Meeting, San Diego, CA. December 2009.
"Genome-wide analysis of in vivo translation with single-nucleotide resolution." EMBO Conference on Protein Synthesis and Translational Control, Heidelberg, Germany. September 2009.
"Genome-wide analysis of in vivo translation with single-nucleotide resolution using ribosome profiling." RNA Society Meeting, Madison, WI. May 2009.
"Robustness in Drosophila segment polarity" Complex Biomolecular Networks: Structure, Evolution, and Function, Montauk, NY. September 2005.
"Topology and robustness in the Drosophila segment polarity network." March Meeting of the American Physical Society, Los Angeles, CA. March 2005.
"Topology and robustness in the Drosophila segment polarity network." KITP Microprogram on Networks in Growth, Death, and Aging, Santa Barbara, CA. February 2005.
"Robustness in Drosophila segment polarity." New York Academy of Science Systems Biology Discussion Group, New York, NY. November 2004.
Teaching Experience
Johns Hopkins University

Critical Thinking in Biology

Fall 2011

Marine Biological Laboratory

Teaching Assistant, Physiology Course

July 2008

Harvard University

Head Teaching Assistant, Genomics and Systems Biology

Spring 2003

Teaching Assistant, Introductory Molecular Biology

Fall 2002

Teaching Assistant, Genomics and Systems Biology

Spring 2002

Professional Service
Reviewer for: Nature, Science, Nature Reviews Genetics, Journal of Cell Biology, PNAS, Molecular Systems Biology, PLoS Genetics, RNA, Molecular and Cellular Proteomics, Nucleic Acids Research, Genome Biology, PLoS Computational Biology, PLoS One, BMC Systems Biology, Genetics, Physiological Genomics, Computing in Science and Engineering